Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for VAPB

Basic gene info.	Gene symbol	VAPB
	Gene name	VAMP (vesicle-associated membrane protein)-associated protein B and C
	Synonyms	ALS8\|VAMP-B\|VAP-B
	Cytomap	UCSC genome browser: 20q13.33
	Genomic location	chr20 :56964174-57026156
	Type of gene	protein-coding
	RefGenes	NM_001195677.1, NM_004738.4,NR_036633.1,
	Ensembl id	ENSG00000124164
	Description	VAMP-associated 33 kDa proteinvesicle-associated membrane protein-associated protein B/C
	Modification date	20141219
dbXrefs	MIM : 605704
	HGNC : HGNC
	Ensembl : ENSG00000124164
	HPRD : 09300
	Vega : OTTHUMG00000032840
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_VAPB
	BioGPS: 9217
	Gene Expression Atlas: ENSG00000124164
	The Human Protein Atlas: ENSG00000124164
Pathway	NCI Pathway Interaction Database: VAPB
	KEGG: VAPB
	REACTOME: VAPB
	ConsensusPathDB
	Pathway Commons: VAPB
Metabolism	MetaCyc: VAPB
	HUMANCyc: VAPB
Regulation	Ensembl's Regulation: ENSG00000124164
	miRBase: chr20 :56,964,174-57,026,156
	TargetScan: NM_001195677
	cisRED: ENSG00000124164
Context	iHOP: VAPB
	cancer metabolism search in PubMed: VAPB
	UCL Cancer Institute: VAPB
Assigned class in ccmGDB	C

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Phenotypic Information for VAPB(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: VAPB
	Familial Cancer Database: VAPB

* This gene is included in those cancer gene databases.


Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: VAPB
	MedGen: VAPB (Human Medical Genetics with Condition)
	ClinVar: VAPB
Phenotype	MGI: VAPB (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: VAPB

Mutations for VAPB

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	VAPB	chr20	56979777	56979797	VAPB	chr20	56981528	56981548

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows VAPB related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
XX000009	VAPB	1	67	20	56964507	56964573	IKZF3	66	166	17	37933922	37934022
AW993740	VAPB	1	337	20	56979196	56979533	DMD	331	582	X	31213612	31213863
AI093537	DAXX	24	246	6	4518583	4519208	VAPB	242	420	20	57020285	57020463
BF872158	VAPB	1	136	20	57010521	57010657	VAPB	132	394	20	56999371	56999633

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=19)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr20:57016059-57016059	p.E165K	4
chr20:57016116-57016116	p.R184W	1
chr20:56993269-56993269	p.P21S	1
chr20:57009708-57009708	p.F88V	1
chr20:57016123-57016123	p.E186G	1
chr20:56993271-56993271	p.P21P	1
chr20:57009745-57009745	p.S100*	1
chr20:57019206-57019206	p.K216M	1
chr20:56993278-56993278	p.D24N	1
chr20:57015970-57015970	p.V135A	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample				5			1		1			2	1				3	1		5
# mutation				5			1		1			2	1				3	1		5
nonsynonymous SNV				3					1			1	1				2			5
synonymous SNV				2			1					1					1	1

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chr20:56993269	p.I233I	1
chr20:57015992	p.P21S,VAPB	1
chr20:56993271	p.V234I	1
chr20:57016022	p.P21P,VAPB	1
chr20:56993278	p.V236L	1
chr20:57016033	p.D24N,VAPB	1
chr20:56993321	p.R38Q,VAPB	1
chr20:57016116	p.R50R,VAPB	1
chr20:56993358	p.R51G,VAPB	1
chr20:57016123	p.L73L	1

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for VAPB in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for VAPB

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


ARFGEF2,GID8,FAM217B,RTFDC1,CSE1L,CSTF1,DNAJC5, EEF1A2,LSM14B,NPEPL1,OSBPL2,PPP1R3D,PSMA7,RAB22A, RAE1,SLMO2,SS18L1,STX16,TAF4,NELFCD,VAPB	ALDH5A1,CMBL,CSNK2A3,CUL4A,DCAF5,DCAF8,HBS1L, HECTD1,HSPA9,KIAA0368,L2HGDH,LOC729082,NDUFS1,NRD1, PRKAR2A,SOX6,STAU2,UQCC1,USO1,VAPB,ZFYVE9

GID8,AAR2,RTFDC1,CSE1L,CSTF1,DDX27,DPM1, DSN1,TTI1,MOCS3,RAE1,RPRD1B,SLMO2,SPATA2, STAU1,TAF4,NELFCD,TP53RK,UBE2V1,VAPB,YTHDF1	ARL8B,ASB8,ATL3,ATP5J,ATP6V1E1,MINOS1,CAMTA1, COX6C,DNAJA2,EFR3A,RMDN1,KPNA4,PSMC1,RAB18, RAB6A,RHOA,SBDS,SEC23A,UHRF1BP1L,VAPB,YWHAQ

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for VAPB

There's no related Drug.

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Cross referenced IDs for VAPB

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information